X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmol.java;h=c9f275b56d87ef1c7c2dac1c8be98b96198ed1ad;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=299b70cfe2679807d2b269f58a3e0b5196970514;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmol.java b/src/jalview/appletgui/AppletJmol.java
index 299b70c..c9f275b 100644
--- a/src/jalview/appletgui/AppletJmol.java
+++ b/src/jalview/appletgui/AppletJmol.java
@@ -1,82 +1,124 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.util.*;
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.api.SequenceStructureBinding;
-import jalview.datamodel.*;
-import jalview.structure.*;
-import jalview.io.*;
-
-import org.jmol.api.*;
-
-import org.jmol.popup.*;
-import org.jmol.viewer.JmolConstants;
-
-import jalview.schemes.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FileParse;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.HelixColourScheme;
+import jalview.schemes.HydrophobicColourScheme;
+import jalview.schemes.PurinePyrimidineColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.UserColourScheme;
+import jalview.schemes.ZappoColourScheme;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.TextArea;
+import java.awt.TextField;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.KeyEvent;
+import java.awt.event.KeyListener;
+import java.awt.event.WindowAdapter;
+import java.awt.event.WindowEvent;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
 
 public class AppletJmol extends EmbmenuFrame implements
 // StructureListener,
-        KeyListener, ActionListener, ItemListener, SequenceStructureBinding
+        KeyListener, ActionListener, ItemListener
 
 {
-  Menu fileMenu = new Menu("File");
+  Menu fileMenu = new Menu(MessageManager.getString("action.file"));
 
-  Menu viewMenu = new Menu("View");
+  Menu viewMenu = new Menu(MessageManager.getString("action.view"));
 
-  Menu coloursMenu = new Menu("Colours");
+  Menu coloursMenu = new Menu(MessageManager.getString("action.colour"));
 
-  Menu chainMenu = new Menu("Show Chain");
+  Menu chainMenu = new Menu(MessageManager.getString("action.show_chain"));
 
-  Menu helpMenu = new Menu("Help");
+  Menu helpMenu = new Menu(MessageManager.getString("action.help"));
 
-  MenuItem mappingMenuItem = new MenuItem("View Mapping");
+  MenuItem mappingMenuItem = new MenuItem(
+          MessageManager.getString("label.view_mapping"));
 
-  CheckboxMenuItem seqColour = new CheckboxMenuItem("By Sequence", true);
+  CheckboxMenuItem seqColour = new CheckboxMenuItem(
+          MessageManager.getString("action.by_sequence"), true);
 
-  CheckboxMenuItem jmolColour = new CheckboxMenuItem("Using Jmol", false);
+  CheckboxMenuItem jmolColour = new CheckboxMenuItem(
+          MessageManager.getString("action.using_jmol"), false);
 
-  MenuItem chain = new MenuItem("By Chain");
+  MenuItem chain = new MenuItem(MessageManager.getString("action.by_chain"));
 
-  MenuItem charge = new MenuItem("Charge & Cysteine");
+  MenuItem charge = new MenuItem(
+          MessageManager.getString("label.charge_cysteine"));
 
-  MenuItem zappo = new MenuItem("Zappo");
+  MenuItem zappo = new MenuItem(MessageManager.getString("label.zappo"));
 
-  MenuItem taylor = new MenuItem("Taylor");
+  MenuItem taylor = new MenuItem(MessageManager.getString("label.taylor"));
 
-  MenuItem hydro = new MenuItem("Hydrophobicity");
+  MenuItem hydro = new MenuItem(
+          MessageManager.getString("label.hydrophobicity"));
 
-  MenuItem helix = new MenuItem("Helix Propensity");
+  MenuItem helix = new MenuItem(
+          MessageManager.getString("label.helix_propensity"));
 
-  MenuItem strand = new MenuItem("Strand Propensity");
+  MenuItem strand = new MenuItem(
+          MessageManager.getString("label.strand_propensity"));
 
-  MenuItem turn = new MenuItem("Turn Propensity");
+  MenuItem turn = new MenuItem(
+          MessageManager.getString("label.turn_propensity"));
 
-  MenuItem buried = new MenuItem("Buried Index");
+  MenuItem buried = new MenuItem(
+          MessageManager.getString("label.buried_index"));
 
-  MenuItem purinepyrimidine = new MenuItem("Purine/Pyrimidine");
+  MenuItem purinepyrimidine = new MenuItem(
+          MessageManager.getString("label.purine_pyrimidine"));
 
-  MenuItem user = new MenuItem("User Defined Colours");
+  MenuItem user = new MenuItem(
+          MessageManager.getString("label.user_defined_colours"));
 
-  MenuItem jmolHelp = new MenuItem("Jmol Help");
+  MenuItem jmolHelp = new MenuItem(
+          MessageManager.getString("label.jmol_help"));
 
   Panel scriptWindow;
 
@@ -88,7 +130,8 @@ public class AppletJmol extends EmbmenuFrame implements
 
   AlignmentPanel ap;
 
-  ArrayList _aps = new ArrayList();
+  List<AlignmentPanel> _aps = new ArrayList<AlignmentPanel>(); // remove? never
+                                                               // added to
 
   String fileLoadingError;
 
@@ -128,7 +171,7 @@ public class AppletJmol extends EmbmenuFrame implements
           String[][] boundchains, boolean align, AlignmentPanel ap,
           String protocol)
   {
-    throw new Error("Not yet implemented.");
+    throw new Error(MessageManager.getString("error.not_yet_implemented"));
   }
 
   public AppletJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
@@ -136,10 +179,8 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     this.ap = ap;
     jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
-            new PDBEntry[]
-            { pdbentry }, new SequenceI[][]
-            { seq }, new String[][]
-            { chains }, protocol);
+            new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
+            new String[][] { chains }, protocol);
     jmb.setColourBySequence(true);
     if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
     {
@@ -238,7 +279,7 @@ public class AppletJmol extends EmbmenuFrame implements
       dispose();
       return;
     }
-    jmb.newJmolPopup(true, "Jmol", true);
+    // jmb.newJmolPopup(true, "Jmol", true);
 
     this.addWindowListener(new WindowAdapter()
     {
@@ -305,7 +346,8 @@ public class AppletJmol extends EmbmenuFrame implements
           if (freader == null)
           {
             throw new Exception(
-                    "Invalid datasource. Could not obtain Reader.");
+                    MessageManager
+                            .getString("exception.invalid_datasource_couldnt_obtain_reader"));
           }
           jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
                   freader);
@@ -329,20 +371,19 @@ public class AppletJmol extends EmbmenuFrame implements
     jmb.loadInline(string);
   }
 
-  void setChainMenuItems(Vector chains)
+  void setChainMenuItems(Vector<String> chains)
   {
     chainMenu.removeAll();
 
-    MenuItem menuItem = new MenuItem("All");
+    MenuItem menuItem = new MenuItem(MessageManager.getString("label.all"));
     menuItem.addActionListener(this);
 
     chainMenu.add(menuItem);
 
     CheckboxMenuItem menuItemCB;
-    for (int c = 0; c < chains.size(); c++)
+    for (String ch : chains)
     {
-      menuItemCB = new CheckboxMenuItem(chains.elementAt(c).toString(),
-              true);
+      menuItemCB = new CheckboxMenuItem(ch, true);
       menuItemCB.addItemListener(this);
       chainMenu.add(menuItemCB);
     }
@@ -352,9 +393,7 @@ public class AppletJmol extends EmbmenuFrame implements
 
   void centerViewer()
   {
-    Vector toshow = new Vector();
-    String lbl;
-    int mlength, p, mnum;
+    Vector<String> toshow = new Vector<String>();
     for (int i = 0; i < chainMenu.getItemCount(); i++)
     {
       if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
@@ -388,12 +427,7 @@ public class AppletJmol extends EmbmenuFrame implements
       StringBuffer sb = new StringBuffer();
       try
       {
-        for (int s = 0; s < jmb.pdbentry.length; s++)
-        {
-          sb.append(jmb.printMapping(jmb.pdbentry[s].getFile()));
-          sb.append("\n");
-        }
-        cap.setText(sb.toString());
+        cap.setText(jmb.printMappings());
       } catch (OutOfMemoryError ex)
       {
         frame.dispose();
@@ -401,8 +435,9 @@ public class AppletJmol extends EmbmenuFrame implements
                 .println("Out of memory when trying to create dialog box with sequence-structure mapping.");
         return;
       }
-      jalview.bin.JalviewLite.addFrame(frame, "PDB - Sequence Mapping",
-              550, 600);
+      jalview.bin.JalviewLite.addFrame(frame,
+              MessageManager.getString("label.pdb_sequence_mapping"), 550,
+              600);
     }
     else if (evt.getSource() == charge)
     {
@@ -477,7 +512,9 @@ public class AppletJmol extends EmbmenuFrame implements
       for (int i = 0; i < chainMenu.getItemCount(); i++)
       {
         if (chainMenu.getItem(i) instanceof CheckboxMenuItem)
+        {
           ((CheckboxMenuItem) chainMenu.getItem(i)).setState(true);
+        }
       }
 
       centerViewer();
@@ -508,10 +545,12 @@ public class AppletJmol extends EmbmenuFrame implements
     else if (evt.getSource() == seqColour)
     {
       setEnabled(seqColour);
-      jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+      jmb.colourBySequence(ap);
     }
     else if (!allChainsSelected)
+    {
       centerViewer();
+    }
   }
 
   public void keyPressed(KeyEvent evt)
@@ -519,7 +558,7 @@ public class AppletJmol extends EmbmenuFrame implements
     if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
     {
       jmb.eval(inputLine.getText());
-      history.append("\n$ " + inputLine.getText());
+      addToHistory("$ " + inputLine.getText());
       inputLine.setText("");
     }
 
@@ -535,8 +574,8 @@ public class AppletJmol extends EmbmenuFrame implements
 
   public void updateColours(Object source)
   {
-    AlignmentPanel ap = (AlignmentPanel) source;
-    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+    AlignmentPanel panel = (AlignmentPanel) source;
+    jmb.colourBySequence(panel);
   }
 
   public void updateTitleAndMenus()
@@ -547,7 +586,7 @@ public class AppletJmol extends EmbmenuFrame implements
       return;
     }
     setChainMenuItems(jmb.chainNames);
-    jmb.colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+    jmb.colourBySequence(ap);
 
     setTitle(jmb.getViewerTitle());
   }
@@ -602,8 +641,6 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     Dimension currentSize = new Dimension();
 
-    Rectangle rectClip = new Rectangle();
-
     public void update(Graphics g)
     {
       paint(g);
@@ -612,7 +649,6 @@ public class AppletJmol extends EmbmenuFrame implements
     public void paint(Graphics g)
     {
       currentSize = this.getSize();
-      rectClip = g.getClipBounds();
 
       if (jmb.viewer == null)
       {
@@ -620,11 +656,13 @@ public class AppletJmol extends EmbmenuFrame implements
         g.fillRect(0, 0, currentSize.width, currentSize.height);
         g.setColor(Color.white);
         g.setFont(new Font("Verdana", Font.BOLD, 14));
-        g.drawString("Retrieving PDB data....", 20, currentSize.height / 2);
+        g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
+                20, currentSize.height / 2);
       }
       else
       {
-        jmb.viewer.renderScreenImage(g, currentSize, rectClip);
+        jmb.viewer.renderScreenImage(g, currentSize.width,
+                currentSize.height);
       }
     }
   }
@@ -656,11 +694,25 @@ public class AppletJmol extends EmbmenuFrame implements
   {
     for (int i = 0; i < _aps.size(); i++)
     {
-      if (((AlignmentPanel) _aps.get(i)).av.getAlignment() == alignment)
+      if (_aps.get(i).av.getAlignment() == alignment)
       {
-        return ((AlignmentPanel) _aps.get(i));
+        return (_aps.get(i));
       }
     }
     return ap;
   }
+
+  /**
+   * Append the given text to the history object
+   * 
+   * @param text
+   */
+  public void addToHistory(String text)
+  {
+    // actually currently never initialised
+    if (history != null)
+    {
+      history.append("\n" + text);
+    }
+  }
 }